Automated Hydroponic Greenhouses represent novel food production systems which include modules for supervising the cultivated soil, packaging plans, as well as prevention, diagnosis and control of pests and diseases. In this setting, we propose the design and implementation of an Integral Intelligent System called JAPIEST, which is focused on the prevention, diagnosis and control of diseases that a?ect tomatoes (Licopersicum exculentum). Plants are farmed inside hydroponic greenhouses, whose particular conditions of temperature, humidity and nutrient consumption rates can in?uence directly the surge of plagues or diseases. It is relevant to detect and control the occurrence of any given pest or disease because plants are utterly sensitive to variations of environmental conditions and they have a short induced lifecycle. JAPIEST is a novel and valuable tool for farmers to make an early decision of the candidate disease, and then apply a suitable control treatment, based on Integrated Pest Management.